Estimation of focal length when using BLAM
Blams accuracy depends on your line drawing accuracy. Maybe if you would repeat the cube line pixel to pixel it would calculate focal length correctly, but I bet there would still be some minor inaccuracy. As for the mesh reconstruction, even in introduction video is stated, that resulting object will probably not be perfect, so you should expect that. BLAM is not perfect, but certainly changes tens of minutes of tweaking into few minutes of tweaking, so it's not bad at all.